pyproject.toml

[build-system]
requires = ["hatchling"]
build-backend = "hatchling.build"

[project]
name = "Oncodrive3D"
dynamic = ["version"]
description = "Oncodrive3D is a method designed to analyse patterns of somatic mutations across tumors to identify three-dimensional (3D) clusters of missense mutations and detect genes that are under positive selection."
authors = [
    { name = "BBGLab (Barcelona Biomedical Genomics Lab)", email = "bbglab@irbbarcelona.org" },    
    { name = "Stefano Pellegrini", email = "stefano.pellegrini@irbbarcelona.org"}
]

readme = "README.md"
requires-python = ">=3.10"
license = {text = "GNU Affero General Public License v3 or later (AGPLv3+)"}
keywords = ["bioinformatics", "positiveselection", "driversprediction", "bbglab"]
dependencies = [
    "adjusttext==1.1.1",
    "aiohttp>=3.11.10",
    "bgreference==0.7",
    "setuptools==61.2.0",
    "bio==1.7.1",
    "colorcet==3.0.1",
    "daiquiri>=3.3.0",
    "matplotlib>=3.6.2",
    "networkx==2.7.1",
    "pandas==1.4.2",
    "progressbar2==4.0.0",
    "pypdl==1.4.5",
    "pytabix==0.0.2",
    "scikit-learn>=1.3.0",
    "scipy>=1.7.3",
    "seaborn>=0.12.2",
    "statsmodels>=0.13.2",
    "tqdm>=4.67.1",
    "numpy==1.26.4",
]


[project.urls]
Homepage = "https://github.com/bbglab/clustering_3d"
# Documentation = "https://oncodrive3d.readthedocs.io/"
Repository = "https://github.com/bbglab/clustering_3d"
Issues = "https://github.com/bbglab/clustering_3d/issues"


[project.scripts]
"oncodrive3D" = "scripts.main:oncodrive3D"
"Oncodrive3D" = "scripts.main:oncodrive3D"
"oncodrive3d" = "scripts.main:oncodrive3D"
"Oncodrive3d" = "scripts.main:oncodrive3D"

[project.optional-dependencies]
linting = [
    "ruff>=0.8.3",
]

[tool.hatch.version]
path = "scripts/__init__.py"

[tool.hatch.build.targets.wheel]
packages = ["scripts"]

[tool.uv]
package = true

[tool.ruff.lint]
select = ["F"]
ignore = ["F401"]

[tool.ruff]
line-length = 127

[tool.ruff.format]
quote-style = "single"
indent-style = "space"
docstring-code-format = true